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Hugh Cross, PhD
I am a computational biologist with a background in ecology and evolutionary genetics. I work on projects across the tree of life, utilising many kinds of data and multiple approaches. With biodiversity studies as a centerpoint, I have naturally come to specialise in metagenomics research. To study any environment is to study a community of genes engaged in molecular dialogues–both within and between species, and this requires a community of researchers working together. I hope to find this team.
Education
Ph.D., Ecology and Evolutionary Biology
Columbia University
New York, NY
2003
M.Sc., Plant Breeding and Genetics
Colorado State University
Fort Collins, CO
1998
B.A., Anthropology
University of Colorado
Boulder, CO
1993
Support and Awards
Micro- and macroalgae interactions with bacteria and fungi to improve the viability of commercial algae production (MICMAC)
Norwegian Institute for Bioeconomy Research Development Pilot Grants, 1.5 million Norwegian kroner (~$US187,500)
N/A
2016
- With C. Bruckner, N. Nagy
Soils to Satellites
Department of Innovation, Industry, Science and Research, Education Investment Fund (Australia), A$184,568.29
N/A
2012
- with A. Lowe (Chief Investigator), P. Doherty, C. Walker, G. Guerin
Impact of grazing on lichens in Murray Basin
South Australia Native Vegetation Research Grant, A$16,230
N/A
2010
Environmental Genomics: Mining, climate change, water, crime and health
ARC Linkage (Australia), A$498,058.52
N/A
2010
- with A. Cooper (Chief Investigator), Adelson D, Brook B, Facelli J, Stevens M, Paton J, Tuckweng K.
21st Century Taxonomy - DNA barcoding of Grasses
Taxonomy Research Initiative Network (Australia), A$63,000
N/A
2009
Molecular genetics to improve the knowledge of plants in South Australia
DEH Research Partnerships (Australia), A$30,385.04
N/A
2009
Evolution and Domestication in the Genus Sechium
Explorers Club Award, US$1,200
N/A
2002
Genetic Diversity of Chayote
Torrey Botanical Society Graduate Student Award Honorable Mention, US$500
N/A
2002
Origins, Evolution, and Conservation of Crop Plants: A Molecular Approach
Torrey Botanical Society Symposium Support Award, US$2,500
N/A
2002
- with co-organizers T.J. Motley and N. Zerega
Professional & Research Experience
Bioinformatician
Department of Anatomy, University of Otago
N/A
Present - 2017
- Conducting bioinformatic analyses on several projects in the department, including on genome and transcriptome assembly and annotation, gene expression, population and phylogenetic research
- Training staff and students in basic and advanced data analysis methods
Scientist
Department of Forest Health, Norwegian Institute for Bioeconomy Research (NIBIO)
N/A
2017 - 2013
- Primary responsibility was conducting bioinformatic analyses on several projects in the department of Forest Health at the institute, including genome and transcriptome assembly, gene expression, population and phylogenetic research of plants, animals, and fungus, and metagenomics
Molecular Botanist
State Herbarium of South Australia
N/A
2013 - 2008
- Conducted research in all areas of plant and fungal genomics, including genomic, transcriptomic, and bioinformatic applications for biodiversity and ecology
- Main coordinator for DNA Barcoding projects
- Trained and consulted with staff for next generation sequencing research
Affiliate Research Fellow
Australian Centre for Ancient DNA & Australian Centre for Evolutionary Biology and Biodiversity, University of Adelaide, SA, Australia
N/A
2013 - 2008
- Conducted research in ancient DNA of plants and fungi
- Led genetic components for major ecological research projects
Research Associate/Laboratory Manager
Pringle Lab, Dept of Organismic and Evolutionary Biology, Harvard University
N/A
2008 - 2005
- Responsible for setting up and maintaining the facility, training new users, establishing all protocols, and conducting research in molecular evolution, systematics, and population genetics
- Developed molecular markers for AFLP, ISSR, and DNA sequence data analyses of fungi and their plant hosts
- Developed methods for the molecular analysis of soil biota, including fungal-plant interactions, and DNA extraction from historical collections of fungus
Laboratory Manager
Leiden Ancient DNA Facility, National Herbarium of The Netherlands
N/A
2005 - 2003
- Responsible for establishing the facility, ordering equipment, establishing protocols for proper use
- Trained other researchers to use the facility
- Optimized protocols for extraction of DNA from museum materials
Postdoctoral Researcher
Leiden Herbarium, National Herbarium of The Netherlands
N/A
2005 - 2003
- Responsible for extraction, amplification, and sequencing of species of Zehneria and related genera to construct a molecular phylogeny of the genus
- Developed new molecular markers for Cucurbitaceae
- Conducted various projects in ancient DNA research in conjunction with researchers at the herbarium, the University of Leiden, and the Naturalis Natural History Museum
PhD Fellow
Cullman Laboratory for Molecular Systematics Studies, The New York Botanical Garden
N/A
2003 - 1999
- Conducted research in molecular genetics, including molecular sequencing, and molecular marker data (AFLP)
- Trained graduate students, postdoctoral students, and visiting scientists in molecular techniques and analyses
DNA Database Manager and Technician
Cullman Laboratory for Molecular Systematics Studies, The New York Botanical Garden
N/A
2002 - 2001
- Set up the DNA database for the collection at the Cullman Laboratory using Freezerworks software
- Transferred data from lab files and fieldbooks; labeled DNA and dried-silica collections
Publications
Publications Overview:
Citations: 1400
h-index: 14
First mitochondrial genome of the Caucasian squirrel Sciurus anomalus (Rodentia, Scriuridae)
Mitochondrial DNA Part B 6: 883-885
N/A
2021
- Boukhdoud, L., Parker, L.D., McInerney, N.R., Saliba, C., Kahale, R., Cross, H.B., Matisoo-Smith, L., Maldonado, J.E., Bou Dagher Kharrat, M.
First mitochondrial genome of the marbled polecat Vormela peregusna (Carnivora, Mustelidae)
Mitochondrial DNA Part B 6: 1009-1011
N/A
2021
- Boukhdoud, L., Parker, L.D., McInerney, N.R., Saliba, C., Kahale, R., Cross, H.B., Matisoo-Smith, L., Maldonado, J.E., Bou Dagher Kharrat, M.
Genomic sequencing comfirms absence of introgression despite past hybridisation between a common and critically endangered bird
Global Ecology and Conservation 28: e01681
N/A
2021
- Forsdick, N.J., Martini, D., Brown, L., Cross, H.B., Maloney, R.F., Steeves, T.E., Knapp, M.
Genomic screening reveals that the endangered Eucalyptus paludicola (Myrtaceae) is a hybrid
Diversity 12: 468
N/A
2020
- van Dijk, K., Waycott, M., Quarmby, J., Bickerton, D., Thornhill, A.H., Cross, H.B., Biffin, E.
Molecular underpinnings of long-term methyl jasmonate-induced resistance in Norway spruce
Plant Cell & Environment 43: 1827-1843.
N/A
2020
- Magerøy, M., Wilkinson, S., Tengs, T., Cross, H.B., Almvik, M., Petriacq, P., Vivian-Smith, A., Zhao, T., Fossdal, C.G., Krokene, P.
One thousand plant transcriptomes and the phylogenomics of green plants
Nature 574: 679-685.
N/A
2019
- Leebens-Mack, J. et al.
The Sturt pea through 300 years of Australian botanical exploration
Swainsona 30: 1-8.
N/A
2018
- Cross, H.B., Biffin, E., Waycott, M.
Ash dieback in Norway - current situation
In: Dieback of European Ash (Fraxinus spp.) - Consequences and Guidelines for Sustainable Management (Eds: Vasaitis, R. & Enderle, R.), pp. 166-175. COST.
N/A
2017
- Børja, I., Timmermann, V., Hietala, A.M., Tollefsrud, M.M., Nagy, N.E., Vivian-Smith, A., Cross, H.B., Sønstebø, J.H., Myking, T., Solheim, H.
Fungal diversity and seasonal succession in ash leaves infected by the invasive ascomycete Hymenoscyphus fraxineus
New Phytologist, 213(3): 1405-1417
N/A
2017
- Cross, H.B., Sønstebø, J.H., Nagy, N.E., Timmermann, V., Solheim, H., Børja, I., Kauserud, H., Carlsen, T., Rzepka, B., Wasak, K., Vivian-Smith, A., Hietala, A.M.
Effective application of next generation sequencing (NGS) approaches in systematics and population genetics - case studies in Eucalyptus and Acacia
Australian Systematic Botany 29(3): 235-246
N/A
2016
- Cross, H.B., Biffin, E., van Dijk, K., Lowe, A., Waycott, M.
Molecular phylogenetic analyses of Cucurbitaceae tribe Benincaseae urge for merging of Pilogyne with Zehneria
Phytotaxa, 236(2): 173-183
N/A
2015
- de Boer, H.J., Cross, H.B., de Wilde, J.J.O., Duyfjes, B.E.E., Gravendeel, B.
Using phylogenetic diversity to identify ancient rain forest refugia and diversification zones in a biodiversity hotspot.
Diversity and Distributions 21: 279-289
N/A
2015
- Costion, C. Edwards, W., Ford, A., Metcalfe, D., Cross, H.B., Harrington, M., Richardson, J., Hilbert, D., Lowe, A., Crayn, D.
Global change community ecology beyond species-sorting: a quantitative framework based on mediterranean-biome examples
Global Ecology and Biogeography 23: 1062-1072
N/A
2014
- Guerin, G, Martín-Forés, I, Biffin, E., Baruch, Z., Breed, M., Christmas, M., Cross, H.B., Lowe, A.J.
A spatially predictive baseline for monitoring multivariate species occurrences and phylogenetic shifts in mediterranean southern Australia
Journal of Vegetation Science 25: 338-348
N/A
2013
- Guerin, G.R., Biffin, E., Jardine, D.I., Cross, H.B., Lowe, A.J.
The application of DNA methods to timber tracking and origin verification
IAWA Journal 32 (2): 251-262
N/A
2011
- Lowe, A.J. & Cross, H.B.
Plant DNA barcodes can accurately estimate species richness in poorly known floras
PloS ONE 6(11): e26841
N/A
2011
- Costion, C., Ford, A., Cross, H.B., Crayn, D., Harrington, M., Lowe, A.J.
DNA barcoding of Invasive Species
In Fifty Years of Invasion Ecology: The Legacy of Charles Elton (Ed. Richardson D.). Chapter 22. Wiley-Blackwell, Oxford
N/A
2010
- Cross H.B., Lowe A.J., Gurgel C.F.D.
Distribution and abundance of the introduced ectomycorrhizal fungus, Amanita phalloides, in North America
New Phytologist 185: 803-816
N/A
2010
- Wolfe B.E., Richard, F., Cross, H.B., and Pringle A.
The ectomycorrhizal fungus Amanita phalloides was introduced and is expanding its range on the west coast of North America
Molecular Ecology 18: 817-833
N/A
2009
- Pringle, A., Rachel I. Adams, R. I., Cross, H.B., Bruns, T.D.
The ecological implications of a Yakutian mammoth’s last meal
Quaternary Research 69: 361-376
N/A
2008
- van Geel, B., Aptroot, A., Baittinger, C., Birks, H.H., Bull, I.D., Kompanje, E.J.O., Cross, H.B., Evershed, R.P., Gravendeel, B., Kuperus, P., Nierop, K.G.J., Mol, D., Pals, J.P., Tikhonov, A. N., van Reenen, G., and van Tienderen, P.H.
The use of orchid pollinia or pollinaria for taxonomic identification
Selbyana 29(1): 6-19
N/A
2008
- Singer, R. B., Gravendeel, B., Cross, H.B., Ramirez, S. R.
Assessment of age and greenness of herbarium specimens as predictor for successful extraction and amplification of DNA
Blumea 53: 407-428
N/A
2008
- Erkens, R. H. J., Cross, H.B., Maas, J. W., Hoenselaar, K., and Chartrou, L. W.
Origin and diversification of chayote
In: Darwin’s Harvest: New Approaches to the Origins, Evolution, and Conservation of Crops (Motley, Zerega, and Cross eds.). Columbia University Press
N/A
2006
- Cross, H.B., Lira Saade, R., and Motley, T. J.
Darwin’s Harvest: New Approaches to the Origins, Evolution, and Conservation of Crops
Columbia University Press
N/A
2006
- Motley, T. J., N. Zerega, and H.B. Cross, (editors)
Regulating access to genetic resources: An analysis of selected case studies
Biodiversity and Conservation 12(7), 1511-1524
N/A
2003
- Dávalos, L.M, Sears, R., Raygorodetsky, G., Simmons, B., Cross, H.B., Grant, T., Barnes, T., Putzel, L. and Porzecanski, A.L.
Phenotypic and genetic diversity of chayote germplasm
Proceedings of the 2002 Cucurbitaceae Congress: 138-143
N/A
2002
- Cross, H.B., and Motley, T. J.
Natural History of Mesoamerica
In: Oxford Encyclopedia of Mesoamerican Cultures, Carrasco et al. (editors). Oxford University Press, New York
N/A
2001
- Cross, H.B.
Rainforests of Mesoamerica
In: Oxford Encyclopedia of Mesoamerican Cultures, Carrasco et al. (editors). Oxford University Press, New York
N/A
2001
- Cross, H.B.
Inheritance of resistance to Fusarium wilt in two common bean races
Crop Science 40(4), 954-958
N/A
2000
- Cross, H.B., Brick, M.A., Schwartz, H.F., Panella, L.W., Byrne, P.F.
Teaching Experience
Certified Software Carpentry Instructor
I also run a biweekly bioinformatics help session
Instructor, Workshop in Environmental DNA
University of Otago
Dunedin & Auckland, NZ
Present - 2019
- Designed from bottom up course to teach methods & concepts for eDNA metabarcoding
Instructor, Software/Data Carpentry
University of Otago
Dunedin, NZ
Present - 2018
- Teaching basic and advanced bioinformatic skills using live coding in a team-teaching environment
Instructor, Advanced Bioinformatic Workshops
University of Otago
Dunedin, NZ
Present - 2017
- Teaching applied bioinformatic skills in specific fields, including population genetics and gene expression (RNAseq)
Instructor, Undergraduate honours course (ANAT458)
University of Otago
Dunedin, NZ
2019
- Gave lectures on data analysis for team-taught course to prepare honours students for their research component.
Lecture: Applications of Ancient DNA for archaeology
Leiden University
Leiden, The Netherlands
2004
- Invited lecture
Public Tour: Botanicals for Flavors and Scent
The New York Botanical Garden
New York, NY
2001
- Gave a tour of the Enid A. Haupt Conservatory, focusing on plants in the collection that are used as flavors and scents
Lecture: The evolution of stem and wood structure
The Cooper Union School of Art
New York, NY
2001
- General Botany for undergraduates
Graduate Teaching Assistant
Columbia University
New York, NY
2000 - 1999
- Taught recitation for introductory biology course
- Helped professor design and grade exams
Instructor, Genetics course
Colorado State University
Fort Collins, CO
1998
- Taught midlevel genetics course required for all science majors
- Covered basic and advanced genetics topics, including transmission, population, and molecular genetics
Teaching Assistant, Genetics
Colorado State University
Fort Collins, CO
1998
- Taught laboratory section for genetics course
Teaching Assistant, Physical Anthropology
University of Colorado
Boulder, CO
1993
- Assisted professor in preparing and grading exams
- helped students with material
Teacher, English as a Second Language
University of Guadalajara
Guadalajara, Mexico
1992 - 1991
- Taught English as a second language from beginning to advanced levels to students of all ages
Selected Abstracts and Presentations
Environmental DNA from pāua (Haliotis spp.) in New Zealand reflects common, but not rare, haplotypic variation in a field setting
Presented at the Society for Molecular Biology and Evolution annual meeting (Virtual Meeting)
N/A
2021
- Adams, C.I.M., Hepburn, C., Cross, H.B., Taylor, H.R., Gemmell, N.J., Bunce, M., Jeunen, G-J., Knapp, M.
Origin and evolution of Tuberculosis in New Zealand
Presented at Queenstown Molecular Biology Meeting, Queenstown, NZ
N/A
2019
- Knapp, M., McDonald, S.K., Buckley, H., Kardailsky, O., Aung, H.L., Cross, H.B., Jeunen, G-J., Matisoo-Smith, E., Walter, R., Cook, G.M.
Unraveling phenology: epigenetic memory adjusts bud set and bud burst in Picea
Presented at NorPlantBio, Trondheim, Norway
N/A
2016
- Viejo, M., Carneros, E., Cross, H.B., Lee, Y.K., Yakovlev, I., Fossdal, C.G., Olsen, J.E.
Priming of plant immunity: molecular mechanisms of defense priming in Norway spruce
Presented at 5th International Workshop on the Genetics of Tree-Parasite Interactions, Orleans, France
N/A
2015
- Krokene, P., Fossdal, C.G., Vivian-Smith, A., Cross, H.B., Zhao, T.
Effect of primed conifer defences on a tree-killing bark beetle-fungus complex
Presented at IUFRO Tree Biotechnology Conference, Florence, Italy
N/A
2015
- Fossdal, C.G., Cross, H.B., Vivian-Smith, A., Krokene, P.
Community profiling of ash leaf mycoflora at a stand heavily affected by ash dieback
Presented at seminar Advances in Fungal Genomics, Ås, Norway
N/A
2015
- Cross, H.B., Hietala, A.
Transcriptomic analysis of the spruce bark beetle
Presented at the annual meeting of the Society for Bioinformatics in Northern Europe, Oslo, Norway
N/A
2014
- Cross, H.B., Fossdal, C. G., Vivian-Smith, A., Krokene, P.
Exploring plant genomic biodiversity in South Australia
Presented at the CBA Biodiversity Genomics Conference, Canberra, Australia
N/A
2013
- Cross, H.B., Biffin, E., van Dijk, K. Waycott, M.
Tales from the cryptogams, fungal DNA from museum collections
Plenary speaker at the Fourth International Barcode of Life Conference, Adelaide, Australia
N/A
2011
- Cross, H.B., Pringle, A.
Strangers in a strange land: camel impact on Australian native flora
Presented at the Fourth International Barcode of Life Conference, Adelaide, Australia
N/A
2011
- Cross, H.B., Armstrong, K., Bauman, U., Thomson, V. Jardine, D. Cooper, A.
Utilizing Grass DNA barcodes to Explore Australian Ecosystems
Presented at the International Botanical Congress, Melbourne, Australia
N/A
2011
- Cross, H.B., Murphy, D., Brown, A., Gardner, S., Syme, A., Jardine, D., Cantrill, D., Lowe, A.J.
Paleoecology from the ground up: ancient DNA of fungi
Presented at the International Botanical Congress, Melbourne, Australia
N/A
2011
- Cross, H.B., Cooper, A.
Ancient DNA of a Mammoth’s Last Meal
Invited Seminar Speaker, Department of Geology, Johns Hopkins University, Baltimore, MD
N/A
2007
- Cross, H.B.
Obtaining plant DNA from museum material
Presented at the International Botanical Congress, Vienna, Austria
N/A
2005
- Cross, H.B., Gravendeel, B.
Symposia and Workshops Organised
Environmental DNA Workshop
University of Otago, Dunedin, NZ
N/A
2019
Plant Ancient Biomolecules: Human History and Changing Climates
Symposium at the International Botanical Congress, Melbourne, Australia
N/A
2011
Current Research in Ancient Plant DNA
Symposium at the International Botanical Congress, Vienna, Austria
N/A
2005
- co-organized with Terry Brown
Ancient DNA
Naturalis Museum
Leiden, The Netherlands
2004
Origins, Evolution, and Conservation of Crop Plants: A Molecular Approach
The New York Botanical Garden
Bronx, NY
2002
- Co-organized with Timothy J. Motley and Nyree Zerega
- Sponsored symposium at the Society for Economic Botany annual meeting
Application of Next Generation DNA Sequencing in Environmental Monitoring and Assessment: Current Status and Future Directions
Adelaide University
Adelaide
N/A